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In Biopython, sequences are usually held as Seq objects, which hold the sequence string and an associated alphabet.

This page describes the Biopython Seq object, defined in the Bio.Seq module (together with related objects like the MutableSeq, plus some general purpose sequence functions).
In addition to this wiki page, there is a whole chapter in the Tutorial (PDF) on the Seq object - plus its API documentation (which you can read online, or from within Python with the help command).

If you need to store additional information like a sequence identifier or name, or even more details like a description or annotation, then we use a SeqRecord object instead. These are the sequence records used by the SeqIO module for reading and writing sequence files.

In the above example, we haven't specified an alphabet so we end up with a default generic alphabet. Biopython doesn't know if this is a nucleotide sequence or a protein rich in alanines, glycines, cysteines and threonines. If you know, you should supply this information:

However, watch out because just like the Python string's count, this is a non-overlapping count!

>>>"AAAA".count("AA")2>>> Seq("AAAA", generic_dna).count("AA")2

In some biological situations, you might prefer an overlapping count which would give three for this example.

Nucleotide methods

If you have a nucleotide sequence (or a sequence with a generic alphabet) you may want to do things like take the reverse complement, or do a translation. Note some of these methods described here are only available in Biopython 1.49 onwards.

Complement and reverse complement

These are very simple - the methods return a new Seq object with the appropriate sequence and the same alphabet:

Transcription and back transcription

If you have a DNA sequence, you may want to turn it into RNA. In bioinformatics we normally assume the DNA is the coding strand (not the template strand) so this is a simple matter of replacing all the thymines with uracil: